Description

Native RNA Sequencing Bowtie2 alignment anchored to single-copy 21-mers found in assembly-filtered PCR-free WGS reads

Methods

The native RNA-seq libraries were done on CHM13 cells using oligodT during library prep and sequenced for 150bp paired-end reads.

Reads were trimmed and filtered and then aligned to the T2T CHM13 v1.0 assembly (released on 20200922) using bowtie2/2.3.5.1 with the following parameters:

-N 0

-k 100

Following alignment, the reads were filtered through samtools F1548 to retain properly paired reads only

Following filtering, the reads were anchored to single-copy 21-mers found in assembly-filtered PCR-free WGS reads generated with meryl/1.2 using GenomeBrowser/20180626 overlapSelect with the following parameters:

-overlapBases=21

Display Conventions and Configuration

Data access

Release history

1. 2020-09-22: CHM13 v1.0 release (chm13.draft_v1.0.fasta)

Contacts

• Rachel O'Neill <rachel.oneill@uconn.edu>
• Savannah Hoyt <savannah.klein@uconn.edu>

Credits

Megan Dennis (library prep & sequencing)

Colin Shew (library prep & sequencing)

Rachel O'Neill (mapping & filtering)

Savannah Hoyt (mapping & filtering)

Arang Rhie (Meryl software)